Between the wars, the airfield was a major base for the Belgian Air Force. In early 1940, about half of the Belgian Air Force, were stationed there prior to the Battle of Belgium in May. On the early morning of 10 May, the alarm was sounded, and the pilots at Schaffen Air Base went to their aircraft, thinking it was an exercise. A few minutes later, 50 unidentified aircraft flew over the airfield. At 04:20am Belgian Hawker Hurricanes at the airfield started their engines. 12 minutes later, three Luftwaffe Heinkel He-111s were spotted, not troubled by AAA fire. The 111s strafed the airfield several times. The Belgian aircraft tried to take off through the explosions and fires. Minutes later Me-110s and Dornier Do-17s strafed and bombed the airfield. Four Hurricanes were set on fire, and 6 others were damaged. The roof of the hangar fell in and the aircraft in it were destroyed. By 5:30 AM, only five aircraft remained operational, two Hawker Hurricanes and three Glosters. After the attack, the survivors were flown off and the airfield abandoned.

During the German occupation of Belgium, Sturzkampfgeschwader 1 (StG 1) formed at Schaffen as Erg.Staffel/St.G.1. It operated Ju-87 Stuka dive bombers from the field, attacking British shipping in the English Channel. The Stukas, however, suffered significant losses against RAF fighters over the channel and were withdrawn in August to bases in the Balkans. For the remainder of the occupation, Schaffen was a non-combat airfield of the Flughafen-Bereichs-Kommando 22/XI (Airport-area command 22/XI).

The British Army moved through the Diest area, clearing the occupying German forces north into The Netherlands. Royal Engineers moved into the airfield and it was re-designated as Advanced Landing Ground B-64. It is unknown which RAF units used the field until the German Capitulation in May 1945. Casualties of British 1st Airborne Division (and others) from Operation Market Garden (Arnhem) were evacuated by 93 (Airborne) Composite Company RASC 1st Airborne Division (sometimes under heavy enemy fire) from Diest in September 1944.<paradata.org.uk/units/93-airborne-composite-company-rasc>

After the war Schaffen became the location of the EVS (Elementary Flying School, or in Dutch: Elementaire Vliegschool). In 1950 the EVS left for Air Base Goetsenhoven however. Schaffen Air Base has also been the home of the Training Center for Parachutists (TrgC Para) of the Belgian ParaCommandos since 1946.